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David Zhang
During my PhD, I have developed and applied algorithms that integrate large-scale genetic and transcriptomic datasets to improve the diagnostics rate of rare disease patients. I’m passionate about developing and releasing robust, user-friendly software that empowers geneticists.
Education
Research assistant, part-time PhD, Bioinformatics
University College London
London, UK
Present - 2017
- Thesis: Using transcriptomics to improve the diagnosis rate of rare disease patients.
- The goal of my PhD is to develop and apply statisical methods and software that improve the genetic diagnosis rates using RNA-sequencing.
MSc, Neuroscience
University College London
London, UK
2016 - 2015
- Thesis: The role of mitochondrial dysfunction in Xerodoma pigmentosum
- Grade: Merit (68%)
- Awarded post-graduate support scheme bursary (£10,000)
BSc, Biomedical science
University College London
London, UK
2015 - 2012
- Thesis: Investigating the function of CYFIP1 in the development of rat hippocampal neurons.
- Grade: 2:1 (69%)
H.S.
Queen Elizabeth’s School
Barnet, UK
2012 - 2007
- Grade: Maths (A*), Biology (A*), Chemistry (A*), Sociology (A).
Research Experience
Honorary Researcher (2 months)
Johns Hopkins Bloomberg School of Public Health
Remote
2020
- In collaboration with Leonardo Collado-Torres, we used the recount3 dataset and LIBD samples to study the effect of complex splicing in individuals with neurological disease.
Research Technician
University College London
London, UK
2017 - 2016
- Used R and bash to investigate the effect of genetic variation on the age of onset of dementia and cognition within Down syndrome patients.
Industry Experience
Bioinformatician internship (3 months)
Verge Genomics
Remote
2020
- Detection of aberrant splicing events in complex disease patients.
- Used AWS infrastructure to analyse 100s of RNA-seq samples derived from patients with Parkinson’s disease and amyotrophic lateral sclerosis
Software & programming
Bioconductor packages
N/A
N/A
Present - 2020
Data science blog posts
N/A
N/A
2021
Kaggle town
N/A
N/A
2020
- Organised club to study python and machine learning through tackling kaggle problems.
Data wrangling
Neuroimmunology & CSF Laboratory, NHS
London, UK
2018 - 2016
- Developer and maintainer of data wrangling pipelines that improved the efficiency and standardisation of monthly financial reports.
Teaching Experience
Developing Bioconductor Packages
University College London
Virtual Event
2020
Unit testing using testthat edition 3
rstats club
Virtual Event
2020
- Talk regarding unit testing fundamentals, the importance of testing and new features released in the R package testthat edition 3.
R fundamentals
Clinician Coders
London, UK
2020 - 2018
- Developed materials and lead workshops that aimed to teach R fundamentals to clinicians.
RNA-sequencing for diagnostics
Kings College London
London, UK
2020 - 2017
- Lectured graduate level students about how transcriptomics can be applied in the diagnostic pipeline.
Selected Publications
Megadepth: efficient coverage quantification for BigWigs and BAMs
Bioinformatics
N/A
2021
- Wilks C, Ahmed O, Baker DN, Zhang D, Collado-Torres L, Langmead B. 2021. Megadepth: efficient coverage quantification for BigWigs and BAMs. Bioinformatics.
- Role: R package developer.
- DOI: https://doi.org/10.1101/2020.12.17.423317
Integration of eQTL and Parkinson’s disease GWAS data implicates 11 disease genes
Jama Neurology
N/A
2021
- Kia DA, Zhang D, Guelfi S, Manzoni C, Hubbard L, United Kingdom Brain Expression Consortium (UKBEC), International Parkinson’s Disease Genomics Consortium (IPDGC), Reynolds RH, Botía JA, Ryten M, Ferrari R, Lewis PA, Williams N, Trabzuni D, Hardy J, Wood NW. 2021. Integration of eQTL and Parkinson’s disease GWAS data implicates 11 disease genes. Jama Neurology.
- Role: Co-first author.
- DOI: https://doi.org/10.1001/jamaneurol.2020.5257
Human-lineage-specific genomic elements: relevance to neurodegenerative disease and APOE transcript usage.
Nature Communications
N/A
2021
- Chen Z, Zhang D, Reynolds RH, Gustavsson EK, Garcia-Ruiz S, D’Sa K, Fairbrother-Brown A, Vandrovcova J, International Parkinson’s Disease Genomics Consortium (IPDGC), Hardy J, Houlden H, Gagliano SA, Botiá J, Ryten M. Human-lineage-specific genomic elements: relevance to neurodegenerative disease and APOE transcript usage. Nature Communications.
- Role: Analyst.
- DOI: TBA
Incomplete annotation of disease-associated genes is limiting our understanding of Mendelian and complex neurogenetic disorders.
Science advances
N/A
2020
- Zhang D, Guelfi S, Ruiz SG, Costa B, Reynolds RH, D’Sa K, Liu W, Courtin T, Peterson A, Jaffe AE, Hardy J, Botia JA, Collado-Torres L and Ryten M. 2020. Incomplete annotation of disease-associated genes is limiting our understanding of Mendelian and complex neurogenetic disorders. Science Advances.
- Role: First Author.
- DOI: https://doi.org/10.1126/sciadv.aay8299
Regulatory sites for known and novel splicing in human basal ganglia are enriched for disease-relevant information.
Nature Communications
N/A
2020
- Guelfi S, D’Sa K, Botía J, Vandrovcova J, Reynolds RH, Zhang D, Trabzuni D, Collado-Torres L, Thomason A, Leyton PQ, Gagliano SA, Nalls MA, UK Brain Expression Consortium, Small KS, Smith C, Ramasamy A, Hardy J, Weale ME & Ryten M. 2020. Regulatory sites for known and novel splicing in human basal ganglia are enriched for disease-relevant information. Nature Communications.
- Role: Analyst.
- DOI: https://doi.org/10.1038/s41467-020-14483-x
Genetic variability in response to Aβ deposition influences Alzheimer’s risk.
Brain Communications
N/A
2019
- Salih DA, Bayram S, Guelfi S, Reynolds RH, Shoai M, Ryten M, Brenton JW, Zhang D, Matarin M, Botia JA, Shah R, Brookes KJ, Guetta-Baranes T, Morgan K, Bellou E, Cummings DM, Escott-Price V, Hardy J. 2019. Genetic variability in response to Aβ deposition influences Alzheimer’s risk. Brain Communications.
- Role: Analyst.
- DOI: https://doi.org/10.1093/braincomms/fcz022
Duplication of 10q24 locus: broadening the clinical and radiological spectrum.
Eur J Hum Genet
N/A
2019
- Holder-Espinasse M, Jamsheer A, Escande F, Andrieux J, Petit F, Sowinska-Seidler A, Socha M, Jakubiuk-Tomaszuk A, Gerard M, Mathieu-Dramard M, Cormier-Daire V, Verloes A, Toutain A, Plessis G, Jonveaux P, Baumann C, David A, Farra C, Colin E, Jacquemont S, Rossi A, Mansour S, Ghali N, Moncla A, Lahiri N, Hurst J, Pollina E, Patch C, Ahn JW, Valat AS, Mezel A, Bourgeot P, Zhang D, Manouvrier-Hanu S. 2019. Duplication of 10q24 locus: broadening the clinical and radiological spectrum. Eur J Hum Genet.
- Role: Analyst.
- DOI: https://doi.org/10.1038/s41431-018-0326-9
Genetic variation within genes associated with mitochondrial function is significantly associated with later age of onset of Parkinson disease and contributes to disease risk.
NPJ Parkinson’s Disease
N/A
2019
- Billingsley KJ, Barbosa IA, Bandrés-Ciga S, Quinn JP, Bubb VJ, Deshpande C, Botía JA, Reynolds RH, Zhang D, Simpson MA, Blauwendraat C, Nalls MA, Singleton A, International Parkinson’s Disease Genomics Consortium (IPDGC), Ryten M, Koks S. 2019. Genetic variation within genes associated with mitochondrial function is significantly associated with later age of onset of Parkinson disease and contributes to disease risk. NPJ Parkinson’s Disease.
- Role: Data provider.
- DOI: https://doi.org/10.1038/s41531-019-0080-x
Variation at the TRIM11 locus modifies Progressive Supranuclear Palsy phenotype.
Annals of Neurology
N/A
2018
- Jabbari E, John W, Tan MMX, Maryam S, Pittman A, Ferrari R, Mok KY, Zhang D, Reynolds RH, de Silva R, Grimm MJ, Respondek G, Muller U, Al-Sarraj S, Gentleman SM, Lees AJ, Warner TT, Hardy J, Revesz T, Hoglinger GU, Holton JL, Ryten M and Morris HR. 2018. Variation at the TRIM11 locus modifies Progressive Supranuclear Palsy phenotype. Annals of Neurology.
- Role: Analyst.
- DOI: https://doi.org/10.1002/ana.25308
Conferences
Genomics England Research Conference
N/A
London, UK
2019
- Poster: Predicting disease-causing genes using machine learning
Genomics of Rare Disease
N/A
Cambridge, UK
2019
- Poster: The use of transcriptomics to improve gene annotation
- Poster: Using machine learning to understand and predict genes causing rare neurological disorders
- Awarded prize for the best poster (£100)
International Parkinson’s Disease Genomics Consortium (IPDGC)
N/A
Lisbon, Portugal
2019
- Talk: Incomplete annotation of disease-associated genes is limiting our understanding of Mendelian and complex neurogenetic disorders
European Society of human genetics (ESHG)
N/A
Milan, italy
2018
- Poster: Incomplete annotation of OMIM genes is likley to be limiting the diagnostics yield from genetic tests.
International Parkinson’s Disease Genomics Consortium (IPDGC)
N/A
Reykjavik, Iceland
2018
- Poster: Incomplete annotation of OMIM genes is limiting the diagnostic yield from genetic tests.
World Science Conference Israel (WSCI)
N/A
Jerusalem, Israel
2015
- 1 of 11 UK participants chosen to attend.